Sequence analysis of bacterial DNA in the colon of an Andean mummy

Abstract

We have isolated DNA from 14 tissue samples from the internal organs of an Andean human mummy (10th-11th century A.D.) and have checked the persistence of the original human and bacterial templates using the following main approaches: 1) amino acid racemization test; 2) quantification of mitochondrial DNA copy number; 3) survey of bacterial DNA in the different organs; 4) sequence analysis of bacterial amplicons of different lengths. The results demonstrate that both the original human DNA and the DNA of the bacteria of the mummy gut are preserved. In particular, sequence analysis of two (respectively 100 and 196 bp in length) libraries of bacterial 16s ribosomal RNA gene amplicons from the mummy colon shows that while the shortest amplicons give only modest and biased indications about the bacterial taxa, the longer amplicons allow the identification several species of the genus Clostridium which are typical of the human colon. This work represents a first example of a methodological approach which is applicable, in principle, to many other natural and artificial mummies and might open the way to the study of the structure of the human microbial ecosystem from prehistory to present.

PCR-based detection of non-indigenous microorganisms in ‘pristine’ environments

“…Under certain conditions intact DNA can be preserved in the environment for extremely long periods. Reports of DNA being amplified from ancient samples, such as museum specimens (Higuchi et al, 1984;; ancient Egyptian mummies (Ubaldi et al, 1998) and amber (Cano et al, , 1994Greenblatt et al, 1999), indicates that the ancient DNA was well preserved and protected. Little is known of the stability of exogenous nucleic acids under the conditions found in Antarctic biotopes.…”

Analysis of ancient DNA from coprolites: a perspective with random amplified polymorphic DNA-polymerase chain reaction approach

“…Gene fragments from eukaryotic and prokaryotic organisms have been successfully detected from human bones and tissues (Fricker et al 1997, Ubaldi et al 1998, Gulh et al 1999, Cano et al 2000, Ferreira et al 2000, Zink et al 2001. All of these studies focused on the recovery of aDNA from a specific organism or a determined gene sequence.…”

Persistence and decay of the intestinal microbiota's DNA in glacier mummies from the Alps

“…It has been repeatedly stated that molecular data in palaeomicrobiology should provide details on the microbial ecology of the specimens analyzed; in particular, one should take into account the possible issue of the specimen's contamination and colonization by external environment microorganisms (Rollo and Marota, 1999;Ubaldi et al, 1998).…”

“…As in this gene the conserved regions alternate to highly variable ones, one can, through cloning and sequencing of the PCR products, putatively identify the different bacterial species present in a sample using 16S rRNA gene sequence databases. This method is routinely applied in our laboratory for the analysis of the vestiges of ancient microorganisms associated with mummified human bodies (Cano et al, 2000;Luciani et al, 2006;Rollo and Marota, 1999;Rollo et al, 1994Rollo et al, , 1995aRollo et al, ,b, 2000Ubaldi et al, 1998).…”